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This article is part of the supplement: Proceedings of the Tenth Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics

Open Access Proceedings

Approximating the edit distance for genomes with duplicate genes under DCJ, insertion and deletion

Mingfu Shao and Yu Lin

Author Affiliations

Laboratory for Computational Biology and Bioinformatics, EPFL, Lausanne, Switzerland

BMC Bioinformatics 2012, 13(Suppl 19):S13  doi:10.1186/1471-2105-13-S19-S13

Published: 19 December 2012

Abstract

Computing the edit distance between two genomes under certain operations is a basic problem in the study of genome evolution. The double-cut-and-join (DCJ) model has formed the basis for most algorithmic research on rearrangements over the last few years. The edit distance under the DCJ model can be easily computed for genomes without duplicate genes. In this paper, we study the edit distance for genomes with duplicate genes under a model that includes DCJ operations, insertions and deletions. We prove that computing the edit distance is equivalent to finding the optimal cycle decomposition of the corresponding adjacency graph, and give an approximation algorithm with an approximation ratio of 1.5 + .